Cultures that had become more defined had settlements that were highly developed and complex. A class system emerged, and agricultural processes became more intricate. Animals such as llama, alpacas and vicuñas were domesticated, pastoral life gave way to territorial life, as groups abandoned their migratory lifestyle. The sedentary nature of Andean groups lead to territorial borders. Social order came to the groups; trade grew between groups, and there was a division of labor and a hierarchy, all consolidated around common religion, language, politics and economy. This period of prosperity was followed by the arrival of the Inca.

Not all indigenous groups in the central Andes were at the same stages of development around the time of the arrival of the Inca.  Many indigenous groups fell easily to the Inca, but many resisted as well; the Inca, moving north from Cusco met resistance when they hit the Shyris-Cañari defenses, and they warred with them for years. The Inca eventually defeated and assimilated the central Andean groups, imposing Inca culture, including their language, Quechua, while still allowing groups to practice their beliefs. The Inca also introduced new crops, improved irrigation and built a mass of infrastructure, including roads connecting Quito with Cusco. The fusion of ethnicities led to collective festivals, as well.

When the Spanish arrived and assumed control of the region in the 1530s, one of the major changes was that privately owned land that had become the property of the Inca emperor during Inca rule fell under the Spaniards feudal system of social organization. The ruling, landholding elite took over the central Andean land and the indigenous who lived there. The indigenous were forced to work the land and were made the property of the conquistadores. This was known as the encomienda system of land ownership.

Spanish settlers on indigenous lands in the central Andes defended the territory and indoctrinated the native population, who were poorly paid for their work. Indigenous labor was further exploited under the Mita system, under which they were required to spend a year working for public or private concerns, constructing churches, roads, public buildings, or working in a textile mill. At the time of the Spanish conquest the native population of Ecuador was around 750,000. However, Spanish diseases such as measles and smallpox decimated the Sierra indigenous population during the 16th century. Years after Ecuador achieved independence the indigenous were eventually freed from slavery.

Though Ecuador was predominantly a rural society, central Andes cities such as Quito grew in administrative and bureaucratic power. Today, the majority of Ecuador's indigenous population continues to live in the central Andes, Ecuador's most populous region. Many indigenous groups still reside in small rural communal settlements, growing crops, raising cattle and producing handicrafts, though there is a great deal of migration to cities.

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Inside Matriz de Guaranda church

The history of Ecuador is a history of the indigenous. Stretching back 11,000 years, Ecuador's history involves the confluence of various ethnic groups and varying developments among cultures, and the central Andes has been the focal point of indigenous life. Of the many theories regarding how Ecuador became populated, the dominant theory is that migrants came from Asia via the land bridge across the Bering Sea. Another popular theory is that the first peoples of what would eventually be known as Ecuador migrated across the Pacific and Atlantic Oceans.

The earliest cultures in Ecuador were hunter-gatherer by nature, and resided on the coast and, primarily, in the central Andes (also known as the Sierra or highlands). The central Andes remains the region most heavily populated by indigenous groups in Ecuador. Over time, the migratory hunter-gatherer societies in the Andes became more sedentary and developed social systems and such cultural attributes as early forms of language. Later on, these cultures diversified and specialized further, developing agricultural methods, metallurgy, and weaving and pottery practices.

It was around 800 AD when indigenous cultures were larger and more organized than they had ever been. Indigenous societies in the central Andes were, overall, the most organized in agriculture and commerce. Groups such as the Pasto, Cara, Panzaleo, Puruhua, Cañari and Palta were the biggest groups in the highlands; each possessed their own distinct language. These indigenous cultures were sedentary and ruled by chieftains. They lived on mountainsides and in valleys and relied on agriculture for survival, practicing terrace farming of crops, and using irrigation and a system of year-round irrigation.

The central Andean region became known as the Kingdom of Quito in 980 AD, when the Caras tribe, a coastal indigenous group who had migrated inland, conquered the Quitu, from which the name Quito, Ecuador's capital, is derived. The Kingdom of Quito ruled the highlands for over four centuries, before being absorbed by the Inca empire after years of battles, and later, by the Spanish, after which it was referred to as the Real Audencia, before becoming Quito.

The Caras and Quitus combined to become the Quitu-Caras, or Shyris, and the fusion of the two groups involved an exchange of language and customs. This led to a more stable way of life, including higher productivity, a better political system and a stronger military. The Shyris expanded their territory and met the Puruahaes when they expanded south. The Shyris formed pacts with the Puruhaes and the Cañaris, who lived further south. The Puruhuas were well organized, with laws and a hereditary monarchy. The daughter of the Puruhua's leader, Duchicela, married the daughter of the leader of the Shyris. The Shyris were the most powerful Andean group in Ecuador until the 14th century, when the Puruhua became more dominant. The Cañaris were the third most powerful group in the Andes during that period.

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